The design and construction of unique buildings, facilities and complexes of “modern” architectural forms and constructive solutions in Russia began less than 20 years ago in the conditions of a shortage of national design codes and experience of such construction. Thus these objects were not provided with proper scientific and technical support and structural health monitoring (SHM) systems. Generally only the instrumental monitoring system, based on results of finite element analysis and comparison with measured data allows performing planning activities to prepare for and respond to changes in state of critical structures and drawing conclusions about the actual state and the possibility of further safe operation of the building. Theoretical foundations of methodology of such SHM have been developed. Parameterized finite element models of buildings, special algorithm of adaptation (calibration) in accordance with results of measurements, methodology of measurements of natural frequencies and modal shapes and algorithm of structural evaluation are proposed in this paper. So-called “start” finite element model is normally developed to study the load-bearing capacity of the current version of the project. Parameterized “monitoring-oriented” three-dimensional dynamic finite element model for each significant stage of life cycle of the building (the stages of construction and operation) is constructed or modified, verified and adapted in accordance with the measured data. The main criterion for the adaptation is the correspondence of calculated and measured spectrum of the natural frequencies and mode shapes in the entire frequency range, significant for the assessment of system-wide changes and for identification – localization of possible defects.